{"status":"FAILED","exception":{"type":"CombineArchiveExecutionError","message":"The COMBINE/OMEX did not execute successfully:\n\n  The SED document did not execute successfully:\n  \n    <class 'AssertionError'>:\n    Unable to generate Stoichiometric Matrix! model has:\n    0 reactions\n    0 species\n    what did you have in mind?\n    "},"skipReason":null,"output":"\u001b[0;36mThank you for using runBioSimulations!\u001b[0m\n\n\u001b[0;36m================================================ Loading Singularity ================================================\u001b[0m\n\n\u001b[0;36m=================================================== Set up storage ==================================================\u001b[0m\n\n\u001b[0;36m========================================== Downloading COMBINE/OMEX archive =========================================\u001b[0m\n  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current\n                                 Dload  Upload   Total   Spent    Left  Speed\n\r  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0\r100   139  100   139    0     0    491      0 --:--:-- --:--:-- --:--:--   492\n\r100  2506  100  2506    0     0   6500      0 --:--:-- --:--:-- --:--:--  6500\n\n\u001b[0;36m=========================================== Executing COMBINE/OMEX archive ==========================================\u001b[0m\nINFO:    Using cached SIF image\nlibtk8.6.so: cannot open shared object file: No such file or directory\r\n\r\nPySCeS defaults to matplotlib's TKagg backend if not specified                          in the user configuration file, set \"matplotlib_backend = <backend>\" \r\nMatplotlib interface loaded (pysces.plt.m)\r\nPitcon routines available\r\nNLEQ2 routines available\r\nSBML support available\r\nYou are using NumPy (2.1.2) with SciPy (1.14.1)\r\nAssimulo CVode available\r\nRateChar is available\r\nParallel scanner is available\r\n\r\nPySCeS environment\r\n******************\r\npysces.model_dir = /home/FCAM/crbmapi/Pysces/psc\r\npysces.output_dir = /home/FCAM/crbmapi/Pysces\r\n\r\n\r\n***********************************************************************\r\n* Welcome to PySCeS (1.2.2) - Python Simulator for Cellular Systems   *\r\n*                http://pysces.sourceforge.net                        *\r\n* Copyright(C) B.G. Olivier, J.M. Rohwer, J.-H.S. Hofmeyr, 2004-2024  *\r\n* Triple-J Group for Molecular Cell Physiology                        *\r\n* Stellenbosch University, ZA and VU University Amsterdam, NL         *\r\n* PySCeS is distributed under the PySCeS (BSD style) licence, see     *\r\n* LICENCE.txt (supplied with this release) for details                *\r\n* Please cite PySCeS with: doi:10.1093/bioinformatics/bti046          *\r\n***********************************************************************\r\n \u001b[36mqueued\u001b[0m\n\n  Executed 1 tasks and 2 outputs:\n    Tasks:\n      Succeeded: 0\n      Skipped: 0\n      Failed: 1\n    Outputs:\n      Succeeded: 0\n      Skipped: 2\n      Failed: 0\n\nBundling outputs ...\nCleaning up ...\n\n============= SUMMARY =============\nExecuted 1 SED documents:\n  SED documents (1):\n    Succeeded: 0\n    Skipped: 0\n    Failed: 1\n  Tasks (1):\n    Succeeded: 0\n    Skipped: 0\n    Failed: 1\n  Outputs (2):\n    Succeeded: 0\n    Skipped: 2\n    Failed: 0\n\nThe COMBINE/OMEX did not execute successfully:\n\n  The SED document did not execute successfully:\n  \n    <class 'AssertionError'>:\n    Unable to generate Stoichiometric Matrix! model has:\n    0 reactions\n    0 species\n    what did you have in mind?\n    \nsrun: error: xanadu-72: task 0: Exited with exit code 1\nsrun: Terminating job step 8543309.1\n\n\u001b[0;36m===================================================== Saving log ====================================================\u001b[0m\nCompleted 3.2 KiB/3.2 KiB (40.6 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6721fbaa2e0c0591a7c87a51/rawLog.txt\n\n\u001b[0;36m===================================================== Saving Structured log ==========================================\u001b[0m\nCompleted 4.9 KiB/4.9 KiB (58.9 KiB/s) with 1 file(s) remaining\rupload: outputs/log.yml to s3://files.biosimulations.org/simulations/6721fbaa2e0c0591a7c87a51/outputs/log.yml\n\n\u001b[0;36m================================================== Zipping outputs ==================================================\u001b[0m\n  adding: outputs/ (stored 0%)\n  adding: outputs/log.yml (deflated 65%)\n  adding: outputs/tmp40273/ (stored 0%)\n  adding: outputs/tmp40273/d1.pdf (deflated 39%)\n  adding: outputs/reports.h5 (deflated 95%)\n  adding: rawLog.txt (deflated 63%)\n\n\u001b[0;36m=================================================== Saving HDF5 outputs ==================================================\u001b[0m\nCompleted 18.8 KiB/18.8 KiB (263.6 KiB/s) with 1 file(s) remaining\rupload: outputs/reports.h5 to s3://files.biosimulations.org/simulations/6721fbaa2e0c0591a7c87a51/outputs/reports.h5\n\n\u001b[0;36m=================================================== Saving non-HDF5 outputs ==================================================\u001b[0m\nCompleted 22.6 KiB/44.9 KiB (209.8 KiB/s) with 5 file(s) remaining\rupload: ./_pystmptmp6i738fzi_parsetab.py to s3://files.biosimulations.org/simulations/6721fbaa2e0c0591a7c87a51/_pystmptmp6i738fzi_parsetab.py\nCompleted 22.6 KiB/44.9 KiB (209.8 KiB/s) with 4 file(s) remaining\rCompleted 26.0 KiB/44.9 KiB (218.9 KiB/s) with 4 file(s) remaining\rupload: outputs/plots.zip to s3://files.biosimulations.org/simulations/6721fbaa2e0c0591a7c87a51/outputs/plots.zip\nCompleted 26.0 KiB/44.9 KiB (218.9 KiB/s) with 3 file(s) remaining\rCompleted 31.8 KiB/44.9 KiB (261.6 KiB/s) with 3 file(s) remaining\rupload: outputs/tmp40273/d1.pdf to s3://files.biosimulations.org/simulations/6721fbaa2e0c0591a7c87a51/outputs/tmp40273/d1.pdf\nCompleted 31.8 KiB/44.9 KiB (261.6 KiB/s) with 2 file(s) remaining\rCompleted 36.3 KiB/44.9 KiB (272.4 KiB/s) with 2 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6721fbaa2e0c0591a7c87a51/rawLog.txt\nCompleted 36.3 KiB/44.9 KiB (272.4 KiB/s) with 1 file(s) remaining\rCompleted 44.9 KiB/44.9 KiB (284.5 KiB/s) with 1 file(s) remaining\rupload: ./output.zip to s3://files.biosimulations.org/simulations/6721fbaa2e0c0591a7c87a51/output.zip\n\n\u001b[0;36m====================================== Unzip contents of COMBINE/OMEX archive ======================================\u001b[0m\nArchive:  archive.omex\n  inflating: contents/manifest.xml   \n  inflating: contents/tmp40273       \n  inflating: contents/LEMS_NML2_Ex9_FN.sbml  \n\n\u001b[0;36m====================================== Save contents of COMBINE/OMEX archive ======================================\u001b[0m\nCompleted 641 Bytes/8.5 KiB (7.9 KiB/s) with 3 file(s) remaining\rupload: contents/manifest.xml to s3://files.biosimulations.org/simulations/6721fbaa2e0c0591a7c87a51/contents/manifest.xml\nCompleted 641 Bytes/8.5 KiB (7.9 KiB/s) with 2 file(s) remaining\rCompleted 4.9 KiB/8.5 KiB (48.5 KiB/s) with 2 file(s) remaining \rupload: contents/tmp40273 to s3://files.biosimulations.org/simulations/6721fbaa2e0c0591a7c87a51/contents/tmp40273\nCompleted 4.9 KiB/8.5 KiB (48.5 KiB/s) with 1 file(s) remaining\rCompleted 8.5 KiB/8.5 KiB (76.2 KiB/s) with 1 file(s) remaining\rupload: contents/LEMS_NML2_Ex9_FN.sbml to s3://files.biosimulations.org/simulations/6721fbaa2e0c0591a7c87a51/contents/LEMS_NML2_Ex9_FN.sbml\n\n\u001b[0;36m==================================================== Updating log (2) ===============================================\u001b[0m\nCompleted 6.9 KiB/6.9 KiB (79.7 KiB/s) with 1 file(s) remaining\rupload: ./rawLog.txt to s3://files.biosimulations.org/simulations/6721fbaa2e0c0591a7c87a51/rawLog.txt\n\n\u001b[0;36m================================================== Saving final log =================================================\u001b[0m\n\n\u001b[0;36m=========================================== Post-processing simulation run ==========================================\u001b[0m\n\u001b[0;32mProcess the manifest file in the COMBINE archive ... succeeded.\nRead the manifest and post the files to the API ... succeeded.\nCreate thumbnails from the images specified in the manifest ... succeeded.\nPost thumbnails to the API ... succeeded.\nProcess the SED-ML file in the COMBINE archive ... succeeded.\nPost the SED-ML file to the API ... succeeded.\nProcess and upload the outputs of the simulation run ... succeeded.\nRetrieve the logs of the simulation run ... succeeded.\nPost the logs to the API ... succeeded.\u001b[0m\n\u001b[1;33mProcess the metadata in the COMBINE archive ... failed due to: The metadata of the file could not be found:\nThere was an error in processing the metadata file. More information is available at https://docs.biosimulations.org/concepts/conventions/simulation-project-metadata/. A validation tool is available at https://run.biosimulations.org/utils/validate-metadata.\nPost the metadata to the API ... failed due to: Metadata not found due to a dependent step failing.\u001b[0m\n\u001b[0;36m================================ Run complete. Thank you for using runBioSimulations! ===============================\u001b[0m","duration":2.008107,"sedDocuments":[{"location":"tmp40273","status":"FAILED","exception":{"type":"SedmlExecutionError","message":"The SED document did not execute successfully:\n\n  <class 'AssertionError'>:\n  Unable to generate Stoichiometric Matrix! model has:\n  0 reactions\n  0 species\n  what did you have in mind?\n  "},"skipReason":null,"output":"Archive contains 1 SED-ML documents with 1 models, 1 simulations, 1 tasks, 1 reports, and 1 plots:\r\n  tmp40273:\r\n    Tasks (1):\r\n      sim1_net1\r\n    Reports (1):\r\n      ex9: 3 data sets\r\n    Plots (1):\r\n      d1: 2 curves\r\n\r\nExecuting SED-ML file 1: tmp40273 ...\r\n  Found 1 tasks and 2 outputs:\r\n    Tasks:\r\n      `sim1_net1`\r\n    Outputs:\r\n      `d1`\r\n      `ex9`\r\n  Executing task 1: `sim1_net1`\r\n    Executing simulation ...Check SBML support is at action level 2\r\nSBML file is L2V2\r\n\r\n*******************************************************************\r\nIssues encountered in SBML translation (model processed anyway)\r\nSBML source: /tmp/tmpbpv98eev.xml\r\n*******************************************************************\r\n\r\nNo free species!? ... help I'm confused! \r\n\r\n*******************************************************************\r\n\r\nWriting file: /tmp/tmp6i738fzi.psc\r\n\r\nSBML2PSC\r\nin : /tmp/tmpbpv98eev.xml\r\nout: /tmp/tmp6i738fzi.psc\r\nUsing model directory: /home/FCAM/crbmapi/Pysces/psc\r\n/tmp/tmp6i738fzi.psc loading ..... \r\nParsing file: /tmp/tmp6i738fzi.psc\r\nInfo: No reagents have been fixed\r\nInfo: \"I\" has been initialised but does not occur in a rate equation\r\nInfo: \"SEC\" has been initialised but does not occur in a rate equation\r\nInfo: \"V\" has been initialised but does not occur in a rate equation\r\nInfo: \"W\" has been initialised but does not occur in a rate equation\r\n \r\n \u001b[31mfailed - \r\nUnable to generate Stoichiometric Matrix! model has:\r\n0 reactions\r\n0 species\r\nwhat did you have in mind?\r\n\u001b[0m\r\n    Generating 2 outputs ...\r\n      Generating output 1: `d1` ... \u001b[36mqueued\u001b[0m\r\n      Generating output 2: `ex9` ...","duration":1.736744,"tasks":[{"id":"sim1_net1","status":"FAILED","exception":{"type":"AssertionError","message":"\nUnable to generate Stoichiometric Matrix! model has:\n0 reactions\n0 species\nwhat did you have in mind?\n"},"skipReason":null,"output":"","duration":1.100804,"algorithm":null,"simulatorDetails":null}],"outputs":[{"id":"d1","status":"SKIPPED","exception":null,"skipReason":null,"output":"","duration":0.464915,"curves":[{"id":"curve_V","status":"SKIPPED"},{"id":"curve_W","status":"SKIPPED"}]},{"id":"ex9","status":"SKIPPED","exception":null,"skipReason":null,"output":"","duration":0.063403,"dataSets":[{"id":"ex9_time","status":"SKIPPED"},{"id":"ex9_V","status":"SKIPPED"},{"id":"ex9_W","status":"SKIPPED"}]}]}]}